Release: merge develop into master#147
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AndrewSazonov merged 10 commits intomasterfrom Apr 9, 2026
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#139) * Refactor type annotations to remove explicit numpy types in multiple files * Enable RSE and SLOT rules * Enable PYI rule and apply some formatting * Enable PT rule * Enable FA, INP, ISC, LOG rules * Enable EM rules * Enable COM rule * Enable C4 rule * Enable PLE, PLW, ASYNC rules * Fix PLC0415 and PLC2801 ruff errors with targeted noqa * Enable UP rule * Enable TRY rule * Enable PERF rule * Update Python version compatibility to 3.12 and adjust related configurations * Fix np.array to np.ndarray in type annotations * Add repository name to GitHub action configuration * Add additional Conda dependencies for osx-arm64 platform * Update GitHub Actions workflow to add concurrency and conditional execution * Correct typo: from "Crystall" to "Crystal"
* Add architecture design document for sequential fitting feature * Improve architecture design document for sequential fitting feature * Update sequential fitting design * Final update sequential fitting design * Accept list of experiments in Fitter.fit instead of collection
* Replace uid_map with direct parameter references in aliases * Auto-enable constraints on create, add enable/disable API * Implement Project.load() from CIF directory * Encode free flags via CIF uncertainty brackets * Update notebooks * Update serialization process to apply constraints before saving project * Move CIF loop truncation from persistence to display methods * Add CIF round-trip integration tests for experiments and structures * Add new integration test * Move analysis.cif into analysis/ directory * Add destination parameter to extract_data_paths_from_zip * Add missing Returns sections to docstrings * Add sequential fitting infrastructure with CSV output * Unify plot_param_series to read from CSV with snapshot fallback * Add multiprocessing support to fit_sequential * Write results.csv from existing single-fit mode * Add apply_params_from_csv for dataset replay * Prevent spawn re-import of __main__ in parallel fit_sequential * Support negative indexing and force recalc in apply_params_from_csv * Add extract_project_from_zip helper function * Refactor extract_project_from_zip call to use zip_path variable * Refactor notebook cell IDs and update project loading process * Remove CSV writing from fit() to fix sequential crash recovery * Fix extract_project_from_zip to find project.cif from zip contents
* Replace uid_map with direct parameter references in aliases * Auto-enable constraints on create, add enable/disable API * Implement Project.load() from CIF directory * Encode free flags via CIF uncertainty brackets * Update notebooks * Update serialization process to apply constraints before saving project * Move CIF loop truncation from persistence to display methods * Add CIF round-trip integration tests for experiments and structures * Add new integration test * Move analysis.cif into analysis/ directory * Add destination parameter to extract_data_paths_from_zip * Add missing Returns sections to docstrings * Add sequential fitting infrastructure with CSV output * Unify plot_param_series to read from CSV with snapshot fallback * Add multiprocessing support to fit_sequential * Write results.csv from existing single-fit mode * Add apply_params_from_csv for dataset replay * Prevent spawn re-import of __main__ in parallel fit_sequential * Support negative indexing and force recalc in apply_params_from_csv * Add extract_project_from_zip helper function * Refactor extract_project_from_zip call to use zip_path variable * Refactor notebook cell IDs and update project loading process * Remove CSV writing from fit() to fix sequential crash recovery * Fix extract_project_from_zip to find project.cif from zip contents * Add unit tests * Add functional tests * Add unit tests * More tests * Add more tests * Replace deprecated loadData with load_data from diffpy * Suppress specific warnings in pyproject.toml for better test output * Enable RUF rules and fix all 297 violations * Enable PRL rules (phase 1) * Use ruff default PLR thresholds with max-args=6 * Refactor FitResults to fix PLR complexity violations in reporting.py * Remove verbosity param from Experiments.add_from_data_path * Move data-loading print from ExperimentFactory to collection * Fix plotting tests and add numpy conversion in _prepare_powder_context * Update tests, tutorials, and docs to use analysis.display API * Reduce McCabe complexity for C90 rule compliance * Fix all FURB rule violations * Fix all PIE rule violations * Fix all BLE001 blind-except violations * Add test-all task * Fix tutorial * Update diagrams and clean up * Harden pickle and urlopen against security audit findings * Increase integration test coverage * Add unit test coverage for utils.py helper functions * Update coverage.yml to refine workflow triggers and concurrency settings * Add unit tests to improve patch coverage for changed files
* Update save_as paths to include 'data/' directory and adjust test function to use temporary directory * Add crysfml * Update notebooks * Clean up * Add simple integration test for crysfml * Bump pycrysfml to 0.2.1 * Add pytest marker to neutron_pd_cwl_lbco_crysfml test * Extend package test script by adding pycrysfml * Fix scipp integration test * Move jupyterlab and pixi-kernel out from pyproject.toml * Remove unnecessary libcxx addition for osx-64 in test.yml * Add custom PyPI index support for pycrysfml in test.yml * Update .gitignore to include data directory for tutorial runtime * Apply latest templates * Add temporary rule ignores for docstring and datetime checks in pyproject.toml * Apply new templates * Update index hash for data integrity in utils.py * Add reverse flag to fit_sequential for reverse-order processing
) * Update save_as paths to include 'data/' directory and adjust test function to use temporary directory * Add crysfml * Update notebooks * Clean up * Add simple integration test for crysfml * Bump pycrysfml to 0.2.1 * Add pytest marker to neutron_pd_cwl_lbco_crysfml test * Extend package test script by adding pycrysfml * Fix scipp integration test * Move jupyterlab and pixi-kernel out from pyproject.toml * Remove unnecessary libcxx addition for osx-64 in test.yml * Add custom PyPI index support for pycrysfml in test.yml * Update .gitignore to include data directory for tutorial runtime * Apply latest templates * Add temporary rule ignores for docstring and datetime checks in pyproject.toml * Apply new templates * Update index hash for data integrity in utils.py * Add reverse flag to fit_sequential for reverse-order processing * Update tutorials index * Update tutorial * Add initial structure and analysis configuration files * Fix asymmetry and save/restore peak_profile_type in experiment CIF * Refactor switchable-type restore into _restore_switchable_types * Update test example * Update data-index.json known hash in utils.py
* Update save_as paths to include 'data/' directory and adjust test function to use temporary directory * Add crysfml * Update notebooks * Clean up * Add simple integration test for crysfml * Bump pycrysfml to 0.2.1 * Add pytest marker to neutron_pd_cwl_lbco_crysfml test * Extend package test script by adding pycrysfml * Fix scipp integration test * Move jupyterlab and pixi-kernel out from pyproject.toml * Remove unnecessary libcxx addition for osx-64 in test.yml * Add custom PyPI index support for pycrysfml in test.yml * Update .gitignore to include data directory for tutorial runtime * Apply latest templates * Add temporary rule ignores for docstring and datetime checks in pyproject.toml * Apply new templates * Update index hash for data integrity in utils.py * Add reverse flag to fit_sequential for reverse-order processing * Update tutorials index * Update tutorial * Add initial structure and analysis configuration files * Fix asymmetry and save/restore peak_profile_type in experiment CIF * Refactor switchable-type restore into _restore_switchable_types * Update test example * Update data-index.json known hash in utils.py * Return numpy array from CrysfmlCalculator and adjust pattern length handling * Add aliases and constraints for isotropic displacement parameters refinement * Add fit command to CLI * Update notebooks * Add CLI documentation to User Guide * Update documentation to move Command-Line Interface section * Bump dependencies * Add back the lost doc file * Re-copy templates * Update installation instructions and CI workflow for macOS support
* Reorganize tmp/ directory * Implement parameter correlations table/plot * Enhance correlation heatmap with threshold and precision parameters for labels * Refine documentation and examples * Refactor example notebooks to improve clarity * Temporarily lower minimum coverage percentage requirement from 75 to 70 * Remove show_diagonal and triangle from plot_param_correlations * Fix PlotterBase.plot_correlation_heatmap lint errors * Fix future annotations, dead code, and **kwargs in display * Clean up
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #147 +/- ##
==========================================
+ Coverage 82.04% 89.31% +7.27%
==========================================
Files 133 134 +1
Lines 6916 7700 +784
Branches 581 723 +142
==========================================
+ Hits 5674 6877 +1203
+ Misses 1037 593 -444
- Partials 205 230 +25
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This was referenced Apr 9, 2026
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This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from
developintomaster.[bot] releaseand is excluded from release notes and version bump logic.